I am disappointed that this thread is so unpopular. I was considering a reinstall and hoping to find a bunch of cool mods to try.

Unlimited respec is the only "cheat" mod I recommend. Cheats in ToME tend to be ego-destroying since you can cheat your ass entirely off and still lose. Unlimited respec is very handy though, since point allocation is so critical... it helps you avoid some very irritating restarts.

Verbose enemies can be fun, but it also is the kind of mod you'll probably want to disable after a few games,

I remember liking the generalist class pack mod, but most of the stock classes are well-balanced so it's the kind of thing that might just complicate your level-ups by filling your interface with crap you don't want or need. (I tend to lean on alchemist talents regardless.) Generalist class pack can also lead you to the unenviable situation of having an ability granted by two different talent trees on the same character, so look ahead.

If you're as persistently bad at roguelikes as I am, Marson's Character Recycler is essential.

Me too, I'll add in a few. From what I've used in general, the biggest addons are made by HousePet. They're pretty well thought out, updated regularly, and best of all you can turn certain aspects off if you don't like them (if you're looking for options, they're in game options under Gameplay but I've found they only show up during a game). Best ones include:

-Arcanum, which adds a whole bunch of interesting magic related things. Three new mage classes, some new common weapons (Ritual Blades which are knives that work off of Dexterity and Magic, and Wardstones which are basically a kind of damage reducing offhand weapon for those who don't really want to use shields), new runes, new trees for Alchemist and Archmage, Alchemists can start the alchemy quests from the start themselves, and a school of magic that can teach any non-antimagic character certain spell trees both old and new. One of these trees is rewarded for completing Storming the City by the magic route, making things a little more even on this quest.

-Midnight is an addon featuring Celestials, though not as bit as Arcanum. It adds two new classes, two races, Chants/Hymns get a rework, a whole bunch of new celestial trees, a new starting area for those who'd rather an easier way to begin, and it throws in scepters to common drops for good measure, which are weapons that calculate damage from Constitution and Magic (these may or may not be useful, I turned them off). Weirdly, there's also a couple other minor addons that require Midnight for one reason or another.

-Verdant features Wilders, and is about as big as Midnight but arguably features many more changes to non-Wilder gameplay than it. More infusion options, two new classes in Wilders, a new Rogue class, a slight Summoner rework, and some new trees for Wyrmic as well as a better first talent for Fire Drake (some are unlocked at start, some that unlock upon certain events). This addon works really well in tandem with Arcanum really: Druids can benefit from Arcanum, the Druid's Herbalism tree is both in Arcanum's Alchemist and in the academy, and the combination of the two's new runes, infusions, and egos balance the two.

As for minor things, I've found these nicely done outside of what I mentioned in the OP:
Hexkin Race (it's a fox, entertaining generics aside it plays pretty interestingly)
Blighted Class (Afflicted class that has some Psionic abilities, and focuses on Mind and Blight damage.)
-Wraith Race (A ghostly undead race)
-Vampire race (Undead race that learns Necromancy as it's racials hit level 5. Also comes with a Sunwalker version that revolves around positive energy trees, but Midnight is required for it.)
-Commando class (Basically, it's Rambo. Revolves around unnarmed fighting, stealth, and one-handed weapons. Notable for coming with a bandanna that was actually already in the game.)
-Necromancy+ (A HousePet addon mostly revolving around Necromancer a better class. Also adds in a Spiritmancer summoner/mage class and gives Shadowblade and Doomed a tree or two.)
-Eternal Darkness (Another Necromancer tweak. Adds in a vampirism tree, some locked trees, and regulates Lichform to generics. They're both different takes on the idea, but I like ED a little better. This one's the only one of the two that will work with Deathknight.)
-Spellsword class (This addon started out as an Arcane Blade tweak, and it ended up a whole new class of Mage/Warrior. Each tree revolves around a certain stance and weapon setup, but it's done in a way that you can find synergy with the right items. Pretty fun mechanics as you'll want to have more than one tree.)
-Prowler class (a Rogue/Wilder hybrid that can use either Mindstars or Daggers proficiently. If you're using Verdant you may or may not be interested in this one because of Werebeast and Woodsman already offering takes on this.)
-Pepper Pack (adds a bunnymorph race, some new weapons, the new damage type of Sound, the Bard class which plays as a jack of all trades, and adds a Sound/Light magic tree to Shadowblade. Not bad and Rapiers are useful, but Harps and Singing Swords have quite the limited use for common drops.)
-Nullpack (Adds a huge amount of classes focused on being hybrids. There's some interesting ideas and additions to metaclasses that aren't dealt with by addons very often like Psionic. It tends to conflict with the bigger addons however.)

I've been playing Skirmishers using the Kobold add-on race, and the new weapon types mod. (Bucklers!) The +6 dex is pretty extreme and makes for an easy early game, especially if you invest in bite for taking down enemies that make it to your side... but by midgame more than 1 point in bite (to unlock the next talent) is a waste of generics.

Go To Landmark - Will show you or guide you to a town or dungeon that you saw. Still playing with it, but I have more than once spent 20+ minutes hunting for a particular dungeon and this helps alleviate having to do that. It will also tell you where an unopened chest is in a particular level. Which is nice for me since I try to leave chests for last and like dungeons, sometimes have to spend a bit of time hunting for them.

It doesn't appear to do the same for unopened vaults. But again, still playing with it. The only thing I wish it did was be part of the right click menu on the map instead of having to hit escape where it's cluttered with all the other options. But it's not a huge deal for me since this isn't something I will fully rely on.

Cloak Reminder - If you play undead, reminds you to put your shirt on when going out in public. Does what it says. Semi-helpful if you like to take the cloak off now and then.

I've had a bit of fun playing Gladiator lately. It's a different take on a warrior class, focusing on what weapons you're using and what style you'r e playing with. Each tree focuses on a different kind of weapon (Swords/Greatswords, Maces/Greatmauls, Waraxes/Battleaxes, and an unlockable Whip/Trident tree), and it's done in a way to where a lot of talents have different buffs according to what style you're wielding them in and passives have always active buffs for such: a weapon in each hand, a weapon and shield, or a two-hander (a 1 hander in each hand is available form the start like on Reaver, though it isn't always automatically the best choice), all three have advantages in this class. There's also passive trees of course, one of which revolves around quick switching weapons to take advantage of more than one kind.

It's a pretty darn fun take on the Warrior metaclass as a whole, really. I've always kinda wondered why the three main weapon types that fall under Weapons Mastery weren't a little more different, and this class helps that by proxy.

EDIT: Also, Enhanced Object Compare and Enhanced Wield Replace are nigh irreplaceable once you start using them. The Rune/Infusion comparison mode doesn't seem to work with added ones however (Verdant and Arcanum for example), but this is minor.

I like very much this thread. I will try some addons. Thank you.

The guy behind Gladiator recently made a White Monk class. If the name sounds familiar, yes it does have some similarities to the Final Fantasy series's class (not the first reference either, Stoic had a few name references to Tactics). Unlike the last Brawler hybrid in the Nullpack however, this plays completely different to the mainline unarmed class.

Unlike Brawler you don't have Striking Pose anymore, and no combos at all. Instead you have a wealth of attacks that revolve around channeling your attacks at a range, recovery of both health and stamina (as well as a gradual healing tree this also includes Skirmisher's sole Will based tree), and comparatively only a small amount of close combat moves. Unarmed mastery is a class talent, and like Wyrmic class talent investment will do a general boost in status as well.

Make the game easier / avoid annoying "unlucky" restarts

Escorts Enhanced - escorts follow you, heal when resting (I feel this is simply good design because it's the weaker classes which have trouble keeping escorts alive)
Select your Escorts - choose escort class (again, weaker classes need specific escorts more)
Logical Alchemists - quest alchemists preferentially complete potions you're not helping them with (if I don't get 4 talent points, it's restart o'clock)
Alchemy Woes: Only One Provider - complete all potions (cheesy alternative to the above)


Interface

Impending Dialog - popup window when getting Impending Doom
Plenum Tooltip - better enemy descriptions

ZOmnibus Addon Pack - many interface enhancements and some "cheats", notably:

Inventory Sort Order - better sorting, similar items grouped together
Store Wish List - mark items in stores as wishes, view wishlist from anywhere, get popups when you have enough money (helps to keep track of best inscriptions)
Notes to Self - notes pop up on loading save
Talent Point Planner - plan a character and reference your plan, including when assigning points
Prodigious Progress - show prodigy requirements progress
Pragmatic Heroism - show exact hit points while below 0.
Opt-in Adventurers Parties - decide whether to fight adventurer patrols. Orc patrols chase you so it doesn't work on them all that well (yes, orcs are easy, but they're bloody annoying).
Alternate Zones Option - ban or force alternate zones. Less cheesy now that (1.5.0) zone levels reset on entry and it's possible to check almost every zone that matters straight away. I ban alt sandworm and force alt maze.